Collaborative Software Engineering Workshop

Richard M. Keller, Ph.D.

ScienceOrganizer:A Collaborative Information

Management Tool for Scientific Teams

Information Sharing and Integration GroupCollaborative and Assistant Systems Tech Area

Computational Sciences DivisionNASA Ames Research Center

Rich KellerShawn WolfeDavid Hall, QSSRobert CarvalhoSteve Rich, SAICDeepak KulkarniDan Berrios, RIACS

ScienceDesk Project Staff

Computational Sciences DivisionNASA Ames Research Center

Sergey Yentus, QSSKeith SwansonIan Sturken, QSSLing-Jen Chiang, QSSDavid NishikawaLinda Andrews, RIACS

WWW

Information archiving andsharingImages, Models, Documents, Data, Notes, plusorganization, retrieval, indexing, annotation,and threading services

Collaboration/Coordination/Communication ServicesConsultation tools, Workflow, Calendars, Group and ResourceScheduling, Awareness, Email distribution and archiving,Video/audio conferencing, Chat

Remote control ofScientific InstrumentsMonitoring, control, and experimentation

WWWWWW

WWW

Internet

Internet

Internet

Internet

ScienceDesk Project:ScienceDesk Project: Infrastructure Infrastructuresupport for distributed scientific teamssupport for distributed scientific teams

Research Areas

•• Scientific Knowledge Management Scientific Knowledge Management: : capture,capture,

preservation, traceability of scientific knowledgepreservation, traceability of scientific knowledge

•• Intelligent Information AccessIntelligent Information Access: : intelligent indexing,intelligent indexing,

visualization, and navigationvisualization, and navigation

•• CollaboratoriesCollaboratories: : asynchronous and synchronous asynchronous and synchronous

collaborative scientific teamworkcollaborative scientific teamwork

•• Agent-assisted Remote ExperimentationAgent-assisted Remote Experimentation: :

intelligent monitoring and controlintelligent monitoring and control

http://sciencedesk.arc.nasa.gov

Field Research Sites

Home Institutions

Field Data Collection & Preliminary Data Analysis

U. Conn

Ames Research Center

Field Samples

Geological Samples

Biological Samples

Microbial Cultures

Other culturecollections

YellowstoneNational Park

Microscopy Lab

Greenhouse

Baja California,Mexico

Highborne Cay,Bahamas

U. Miami

Arizona State

Portland State

MicrobialCulture Facility

Microbiology Lab

Motivation: Distributed ScientificField and Lab Work

U. of Oregon

• field notes• images• measurements• sensor data

• lab notes and experiment data• electron microscope images• analysis results• publications

ScienceOrganizer InformationRepository

Field Research Sites

Home Institutions

U. Conn

Ames Research Center

YellowstoneNational Park

Microscopy Lab

Greenhouse

Baja California,Mexico

Highborne Cay,Bahamas

U. Miami

Arizona State

Portland State

MicrobialCulture Facility

Microbiology Lab

U. of Oregon

Central Repository

• Images• Measurements• Cultures• Datasets• Documents• Records

What is ScienceOrganizer?

• An information repository / digital library for distributedscientific project teams: stores heterogeneous projectinformation products -- images, datasets, documents, andvarious types of scientific records (describing samples, field sites,measurements, instruments, microbial cultures, etc.)

• A hybrid tool combining the functionality of:• a database• a document-sharing system• a hypermedia information space• a semantic network

• Features cross-linkage: enables rapid access tointerrelated information

• A “project memory” system: tracks history of projectteam’s fieldwork, labwork, and associated data collectionactivities

The ScienceOrganizer“Project Information Web”

ScienceOrganizer maintains project information inan interconnected network or “information web”

project

image

measurementsite

instrument

sample

document

• Nodes: information resources• Links: relationships among resources

Semantic hypermedia system

Information Resources (“nodes”)

• Describe various types of project-specific information:People, Places, Events, Devices, Measurements

(e.g., field sites, labs, trips, samples, images, documents, instruments etc.)• Contain metadata (categorical, text, or numeric)• Can have “attached” files (e.g., images, documents, datasets)

Microbial-Mat-Sample -654Collected-by: S. Jones

Collection date: 1/24/00Collection site: Pond 6:

field4: …Microbial-Culture-123

Cultivated-by: R. Smith

Genus: microcoleus ch.

Growth medium: ASN

Date isolated: 03-04-00field5: ...

SEM-Image -654

Taken-by: R.SmithImage date: 1/24/00

Equipment:Image File:

Examples of Information Resources:

Information Resources

project

measurement noteimage

document

culture

person

site

sample

experiment

equipment

camera

gas chromatograph

stub

O2 microsensor

N2 microsensor

photographic image

SEM image

SEM

O2 concentration

N2 concentration

Types of ScienceOrganizer“Information Resources” (partial)

spectrometer

spectrograph

chromatogram

other

other

other

micrograph

Relationships among Resources(“links”)

• Information Resources are interrelated by means of named linksthat characterize the nature of the relationship• Relationships are customized to a project team based on an analysisof the information resources in the scientific domain

Microbial-Mat-Sample -654

Collected-by: S. JonesCollection date: 1/24/00

Collection site: Pond 6:field4: …

Microbial-Culture-123Cultivated-by: R. Smith

Genus: microcoleus ch.

Growth medium: ASN

Date isolated: 03-04-00field5: ...

SEM-Image –123x

Taken-by: R.SmithImage date: 1/24/00

Equipment:Image File:

cultivated-fro

m

pictured-in

image sample

culture

photographic image

SEM image

Sanctioned Links between “culture”and other types of resources

stub

equipment

mounted-on

pictured-incultivated-from

person

image (other)

document

has-medium-recipeURL

has-genetic-sequence-URL

isolated-byperson

cultivated-by

Evolving Web of ProjectInformation

member-of site-for

found-atcollected-by

has-measurement

produced-by

cultivated-from

pictured-in

produced-by

has-recipe

project:

site:

document:

sample:

measurement:SEM image:

equipment:equipment:

person:

: culture

EMERG

Brad B. Pond 3 near 4

ASN medium recipe

O2 microsensorSEM

MC-123

SEM image 123xO2 concentration 32B

Project Informationin context

Mat654

Project InformationRecord

Links toRelatedRecords

• images• datasets• cultures• samples• field sites• measurements• instruments• lab notes• publications• spreadsheets

• convenientnavigation

• predefinedlinks

• informationtraceback

create newlinks create new

recordsmodify records

datafields

icon identifiesrecord type

click to navigate

Web-based,platformindependent access

search for records

ScienceOrganizer Browser

Interfacing Software

ScienceOrganizer

SharedImage

Annotator

MicrosensorRemote Controller

sensor

image

annotatedimage

Microsoft Office interface

real-timemeasurements,

images

Agent-assistedScientific

Experimentation System

documents

MarsExploration

Simulator

Sparrow WebInterface

images,measurements

ScienceOrganizer

Shared Image Annotator

Collaborative Whiteboarding & Annotation Tool

MicrosensorMicrosensor Remote Controller Remote Controller

O2 Microsensor &positioning table

ScienceOrganizer

1

2

3

Save to Organizer

Low nutrient Mat from Pond 1A

ScienceOrganizeragent

Experiment DataRepository

Experimentation agent

Science team

Remote controlpositioning table w/instrument package

Agent-assisted ScientificExperimentation System

• overall experiment coordination

Scientist’sagent

Greenhouseagent

• scheduling• error monitoring

• experiment requests • user notification• user preferences

• data storage• logging

ScienceOrganizer

ExperimentSetup/Monitoring

Interface

Pilot Users:• ARC Microbial Ecosystems Group• NAI Ecogenomics Focus Group• ECS Mishap Investigation• ARC Electron Microscopy Lab• JSC Astrobiology Institute for the Study ofBiomarkers

• NIH/NASA Malaria Control Study (viaFundamental Biology Program)

• Mars simulation and analog studies (viaMobile Agents Project)

• ASU/NSF Desert Microbial Survey

ScienceOrganizer Customers

moremature

lessmature

25 10

125Users•Frequent•Moderate•Infrequent

95